Research Skills

Trains single-agent reinforcement learning agents with Stable-Baselines3 — PPO, SAC, DQN, TD3, DDPG, and A2C behind a scikit-learn-like API. Use for standard single-agent RL experiments, quick prototyping, well-documented algorithm implementations on Gymnasium environments, or adding callbacks and evaluation. For high-throughput parallel training, multi-agent systems, or custom vectorized environments prefer alterlab-pufferlib. Part of the AlterLab Academic Skills suite.

Statistical modeling in Python with statsmodels — OLS, GLM, mixed models, and ARIMA with detailed diagnostics, residuals, and inference. Use when fitting specific model classes for econometrics, time series, or rigorous inference with coefficient tables and confidence intervals. For guided statistical test selection with APA reporting prefer statistical-analysis. Part of the AlterLab Academic Skills suite.

Guided statistical analysis with hypothesis-test selection, assumption checking, power analysis, and APA-formatted reporting. Use when choosing the appropriate statistical test for data, verifying test assumptions, computing power/sample size, or producing APA-style results for academic research. For implementing specific models programmatically prefer statsmodels. Part of the AlterLab Academic Skills suite.

Zero-shot univariate time-series forecasting with Google's TimesFM foundation model, producing point forecasts and prediction intervals from CSV/DataFrame/array inputs, with a preflight system checker for RAM/GPU. Use to forecast any univariate series (sales, sensors, energy, vitals, weather) without training a custom model. Part of the AlterLab Academic Skills suite.

Symbolic mathematics in Python with SymPy — solve equations algebraically, perform calculus (derivatives, integrals, limits), manipulate algebraic expressions, work with symbolic matrices, and generate executable code from formulas. Use when exact symbolic results are needed rather than numerical approximations, or for physics, number-theory, and geometry computations involving variables and parameters. Part of the AlterLab Academic Skills suite.

Nonlinear dimensionality reduction with UMAP — fast manifold learning for 2D/3D visualization, clustering preprocessing (e.g., HDBSCAN), and supervised or parametric UMAP. Use when projecting high-dimensional data to low dimensions for visualization, embedding generation, or as a preprocessing step before clustering. Part of the AlterLab Academic Skills suite.

Chunked, compressed N-dimensional arrays for cloud storage with Zarr — parallel I/O, S3/GCS integration, and NumPy/Dask/Xarray compatibility. Use when storing or reading large N-D scientific arrays, streaming chunked data to/from cloud object stores, or building large-scale scientific computing pipelines. Part of the AlterLab Academic Skills suite.

Search the bioRxiv preprint server and retrieve paper metadata or download PDFs via its API. Use when finding life sciences preprints by keywords, authors, DOI, date ranges, or categories, or when conducting a biology literature review of not-yet-peer-reviewed work. Part of the AlterLab Academic Skills suite.

Access the AlphaFold DB of 200M+ AI-PREDICTED protein structures — retrieve models by UniProt accession, download PDB/mmCIF files, and analyze prediction confidence metrics (pLDDT, PAE). Use when a UniProt ID needs a computationally predicted 3D structure or when no experimental structure exists, for homology modeling, protein engineering, or structure-based drug discovery; for EXPERIMENTALLY determined structures (X-ray, cryo-EM, NMR) prefer alterlab-pdb, and for protein sequences, annotations, or accession ID mapping prefer alterlab-uniprot instead. Part of the AlterLab Academic Skills suite.

Search and retrieve preprints from arXiv via the Atom API by keywords, authors, arXiv IDs, date ranges, or subject categories. Use when finding or fetching papers in physics, mathematics, computer science, quantitative biology, quantitative finance, statistics, electrical engineering, or economics, or resolving an arXiv ID to its metadata and PDF. Part of the AlterLab Academic Skills suite.

Query BindingDB for measured protein-ligand binding affinities (Ki, Kd, IC50, EC50) via its keyless REST API or the full TSV download, searching by target (UniProt ID), compound (SMILES), or pathogen. Use when looking up experimental binding constants, profiling inhibitors of a protein target, doing lead optimization, polypharmacology analysis, or structure-activity relationship (SAR) studies; for curated bioactivity mining or drug-like compound library screening at scale prefer alterlab-chembl instead. Part of the AlterLab Academic Skills suite.

Access the BRENDA enzyme database via its SOAP API to retrieve kinetic parameters (Km, kcat, Ki), reaction equations, organism data, and substrate-specific enzyme information indexed by EC number. Use when looking up enzyme kinetics, turnover numbers, or substrate specificity for biochemical research and metabolic pathway analysis. Part of the AlterLab Academic Skills suite.

Query cBioPortal via its keyless REST API for cancer genomics across TCGA, GENIE, MSK-IMPACT and hundreds of studies — somatic mutations, copy-number alterations (GISTIC), mRNA/protein expression, structural variants, and patient-level clinical/survival data. Use when asked how often a gene is mutated/amplified/deleted in a tumor type, to profile oncogenes or tumor suppressors across cancers (pan-cancer alteration frequency), to pull patient-level mutations joined to OS/clinical outcomes, or to validate a cancer target from cohort genomics. For germline variant pathogenicity use alterlab-clinvar; for mutational-signature (SBS) decomposition use alterlab-cosmic; for CRISPR/RNAi gene-dependency use alterlab-depmap; for aggregated target-disease evidence use alterlab-opentargets. Part of the AlterLab Academic Skills suite.

Query ChEMBL via the chembl_webresource_client Python client for curated bioactive molecules and drug-like compound libraries at scale — search compounds by structure or physicochemical properties, retrieve bioactivity measurements (IC50, Ki, EC50), and find inhibitors of a target. Use when screening chemical libraries, mining curated bioactivity for a protein, running SAR studies, or sourcing medicinal-chemistry data; for measured protein-ligand binding affinities (Ki/Kd/IC50) prefer alterlab-bindingdb instead. Part of the AlterLab Academic Skills suite.

Query NCBI ClinVar via the E-utilities API or FTP for the clinical significance (pathogenicity) of human germline genetic variants, searching by gene, variant, condition, or genomic position and interpreting ACMG/AMP classifications and review-status star ratings. Use when assessing whether a variant is pathogenic, likely pathogenic, VUS, likely benign, or benign, resolving conflicting interpretations, or annotating a VCF with ClinVar clinical significance. For population allele frequencies by ancestry use alterlab-gnomad; for somatic cancer mutation frequencies use alterlab-cosmic. Part of the AlterLab Academic Skills suite.

Query ClinicalTrials.gov via its API v2 to search trials by condition, drug, location, recruitment status, or phase and retrieve trial details by NCT ID. Use when finding interventional or observational studies, checking trial status and eligibility for patient matching, or exporting clinical trial records for research. Part of the AlterLab Academic Skills suite.

Access ClinPGx pharmacogenomics data (the successor to PharmGKB) to query gene-drug interactions, CPIC/DPWG dosing guidelines, drug labels, and pharmacogene records. Use when interpreting pharmacogenes (CYP2D6, CYP2C19, TPMT, DPYD, SLCO1B1), looking up genotype-guided drug dosing, checking PGx drug-safety associations (e.g. HLA-B*57:01 and abacavir), or supporting precision medicine and clinical pharmacogenomics decisions. For star-allele definitions/frequencies see PharmVar; for germline/somatic variant pathogenicity see alterlab-clinvar. Part of the AlterLab Academic Skills suite.

Access the COSMIC catalogue of somatic mutations in cancer to query somatic mutations, the Cancer Gene Census, mutational signatures, and gene fusions (authentication required). Use when curating known cancer driver genes, looking up recurrent somatic mutations in a gene, or interpreting mutational signatures for cancer research and precision oncology. Not for germline pathogenicity calls (use alterlab-clinvar) or interactive cohort visualization like OncoPrints and survival from study data (use alterlab-cbioportal). Part of the AlterLab Academic Skills suite.

Query Google Data Commons for public statistical data aggregated from global sources, resolving geographic entities and pulling time-series statistics. Use when working with demographic data, economic indicators, health statistics, or environmental data — population counts, GDP figures, unemployment rates, disease prevalence — or when resolving places to DCIDs and exploring relationships between statistical entities. Part of the AlterLab Academic Skills suite.

Query the Cancer Dependency Map (DepMap) for cancer cell line gene dependency scores (CRISPR Chronos), drug sensitivity data, and gene effect profiles. Use when identifying cancer-specific genetic vulnerabilities, finding synthetic lethal interactions, checking whether a gene is essential in given cell lines, or validating oncology drug targets. Part of the AlterLab Academic Skills suite.

Access and analyze drug information from the DrugBank database — drug properties, interactions, targets, pathways, chemical structures, and pharmacology data. Use when working with pharmaceutical data, drug discovery research, drug-drug interaction analysis, target identification, chemical similarity searches, ADMET predictions, or any task needing detailed drug and drug-target records from DrugBank. Part of the AlterLab Academic Skills suite.

Access the European Nucleotide Archive (ENA) via its API and FTP to retrieve DNA/RNA sequences, raw sequencing reads (FASTQ), and genome assemblies by accession, with support for multiple formats. Use when downloading reads or sequences for a study, run, or sample accession, or when sourcing nucleotide data for genomics and bioinformatics pipelines. Part of the AlterLab Academic Skills suite.

Query the openFDA API for drugs, medical devices, adverse event reports, recalls, regulatory submissions (510k, PMA), and substance identification (UNII). Use when searching FDA safety data, pharmacovigilance and adverse-event signals, device clearances, drug labels, or recall records for regulatory data analysis and safety research. Part of the AlterLab Academic Skills suite.

Query the Ensembl genome database REST API across 250+ species for gene lookups, sequence retrieval, variant analysis, comparative genomics, orthologs, and Variant Effect Predictor (VEP) annotations. Use when mapping gene IDs or coordinates, fetching genomic sequence, finding orthologs across species, or predicting variant consequences for genomic research. Part of the AlterLab Academic Skills suite.

Query NCBI Gene via the E-utilities and Datasets APIs, searching by gene symbol or Gene ID and retrieving gene information (RefSeqs, GO terms, genomic locations, associated phenotypes) including batch lookups. Use when resolving gene symbols to IDs, annotating gene lists, or pulling functional and positional gene metadata for downstream analysis. Part of the AlterLab Academic Skills suite.

Query the GTEx (Genotype-Tissue Expression) portal v2 REST API for tissue-specific gene expression (median TPM across 54 human tissues), expression QTLs (eQTLs), and splicing QTLs (sQTLs). Use when checking which tissues express a gene, finding which gene a non-coding/GWAS variant regulates via eQTLs, or interpreting variant regulatory effects across tissues. NOT for curated trait-variant associations (use alterlab-gwas), population allele frequencies or variant constraint (use alterlab-gnomad), or gene/transcript structure and ID mapping (use alterlab-ensembl). Part of the AlterLab Academic Skills suite.

Query gnomAD (Genome Aggregation Database) for population allele frequencies and gene constraint scores (pLI, LOEUF) reflecting loss-of-function intolerance. Use when checking how common a variant is across populations, filtering rare-disease candidate variants, assessing variant pathogenicity, or identifying loss-of-function intolerant genes. Part of the AlterLab Academic Skills suite.

Access NCBI GEO (Gene Expression Omnibus) for gene expression and functional genomics data — search and download microarray and RNA-seq datasets by GSE, GSM, GPL, or GDS accession and retrieve SOFT, MINiML, and series matrix files. Use when locating public expression datasets, fetching processed expression matrices, downloading a study's supplementary files, or sourcing per-study transcriptomics data for differential-expression analysis. For raw FASTQ sequencing reads by SRA/ENA run accession use alterlab-ena; for reference tissue-expression baselines (median TPM across human tissues) use alterlab-gtex; for cancer cohort somatic mutations and copy-number use alterlab-cbioportal. Part of the AlterLab Academic Skills suite.

Access the Human Metabolome Database (HMDB, 220K+ metabolites), searching by name, HMDB ID, or structure to retrieve chemical properties, biomarker data, NMR/MS reference spectra, and associated pathways. Use when identifying a human metabolite, looking up its biomarker or disease associations, matching NMR/MS spectra, or running metabolomics annotation. Part of the AlterLab Academic Skills suite.

Query the NHGRI-EBI GWAS Catalog REST API for SNP-trait associations, retrieving variants by rs ID, disease/trait, or gene along with p-values and summary statistics. Use when investigating genome-wide association study hits, mapping a SNP or rsID to traits, building polygenic risk scores, or doing genetic epidemiology lookups. Part of the AlterLab Academic Skills suite.

Query the EMBL-EBI InterPro REST API for protein family, domain, and functional-site annotations integrated from member databases (Pfam, PANTHER, PRINTS, SMART, SUPERFAMILY, CDD, ProSite, NCBIfam, and others). Use when predicting protein function, analyzing or comparing domain architecture, classifying a protein by family or homologous superfamily, resolving a Pfam/InterPro accession, or mapping a protein's signatures to GO terms. Not for raw UniProt entry/FASTA retrieval or AlphaFold 3D structures. Part of the AlterLab Academic Skills suite.

Query and download public cancer imaging data from the NCI Imaging Data Commons (IDC) using the idc-index Python package, filtering by metadata, visualizing in-browser, and checking licenses, with no authentication required. Use when obtaining large-scale radiology (CT, MR, PET) or digital pathology DICOM datasets for AI/ML training or cancer imaging research. Part of the AlterLab Academic Skills suite.

Query JASPAR for transcription factor binding site (TFBS) profiles (PWMs/PFMs), searching by TF name, species, or class, scanning DNA sequences for binding sites, and comparing matrices. Use when doing motif analysis, regulatory genomics, transcription factor binding prediction, or interpreting regulatory/non-coding GWAS variants. Part of the AlterLab Academic Skills suite.

Access the NIH Metabolomics Workbench via its REST API (4,200+ studies), querying metabolites, RefMet standardized nomenclature, MS/NMR data, m/z mass searches, and study metadata. Use when retrieving public metabolomics study data, standardizing metabolite names with RefMet, running m/z lookups, or doing biomarker discovery. Part of the AlterLab Academic Skills suite.

Provide direct REST API access to KEGG (academic use only) for pathway analysis, gene-to-pathway and compound-to-pathway mapping, metabolic reactions, KEGG Orthology (KO), drug-drug interactions, and ID conversion. Use when querying KEGG pathways, mapping genes/compounds to metabolic maps, or running KEGG pathway enrichment via raw HTTP/REST; for protein-protein interaction networks prefer alterlab-string-db, for protein sequences and annotations prefer alterlab-uniprot, and for Python workflows spanning many databases prefer bioservices instead. Part of the AlterLab Academic Skills suite.

Query the Monarch Initiative knowledge graph for disease-gene-phenotype associations across species, integrating OMIM, ORPHANET, HPO, ClinVar, and model organism databases. Use when discovering rare disease genes, mapping phenotypes to genes, modeling disease across species, or looking up HPO terms. Part of the AlterLab Academic Skills suite.

Query and analyze scholarly literature using the OpenAlex API across 240M+ works, retrieving papers, authors, institutions, citations, and open access status. Use when searching academic papers, tracking citations, finding works by author or institution, analyzing research trends, discovering open access publications, or running bibliometric analysis. Part of the AlterLab Academic Skills suite.

Query the Open Targets Platform GraphQL API for target-disease associations, tractability and safety data, genetics/omics evidence, and known drugs. Use when identifying or prioritizing therapeutic drug targets, assessing target druggability/safety, or gathering target-disease evidence for drug discovery. Part of the AlterLab Academic Skills suite.

Access the RCSB Protein Data Bank (PDB) for EXPERIMENTALLY determined 3D structures (X-ray, cryo-EM, NMR) of proteins and nucleic acids — searching by text, sequence, or structure similarity and downloading coordinates in PDB/mmCIF format with metadata. Use when retrieving a structure by PDB ID, running sequence or structure similarity searches, or obtaining experimental coordinates for structural biology and drug discovery; for AI-PREDICTED structures of proteins lacking experimental data prefer alterlab-alphafold-db, and for protein sequences, annotations, or accession ID mapping prefer alterlab-uniprot instead. Part of the AlterLab Academic Skills suite.

Query PubChem via the PUG-REST API and PubChemPy across 110M+ compounds, searching by name, CID, or SMILES and retrieving molecular properties, bioactivity, and similarity/substructure matches. Use when looking up a chemical compound, converting names/SMILES to CIDs, fetching physicochemical properties, or running cheminformatics structure searches. Part of the AlterLab Academic Skills suite.

Provide direct REST API access to PubMed via the NCBI E-utilities API, supporting advanced Boolean/MeSH queries, batch processing, and citation management. Use when searching biomedical literature by MeSH terms, retrieving abstracts or PMIDs in bulk, or scripting custom PubMed queries over raw HTTP/REST — for Python workflows prefer biopython (Bio.Entrez) instead, use this for direct REST work or custom API implementations. Part of the AlterLab Academic Skills suite.

Query the Reactome REST API for pathway analysis, over-representation/enrichment, gene-to-pathway mapping, disease pathways, molecular interactions, and expression analysis. Use when running pathway enrichment on a gene list, mapping genes to curated biological pathways, or exploring disease pathways for systems biology studies. Part of the AlterLab Academic Skills suite.

Query the STRING API for protein-protein interactions (59M proteins, 20B interactions across 5000+ species), building interaction networks, discovering functional partners, and running GO/KEGG/Pfam enrichment on protein lists. Use when constructing a protein-protein interaction network, expanding from seed proteins to functional partners, or running PPI-based enrichment for systems biology; for curated metabolic pathway maps and reactions prefer alterlab-kegg, and for protein sequences, annotations, or accession ID mapping prefer alterlab-uniprot instead. Part of the AlterLab Academic Skills suite.

Provide direct REST API access to UniProt (Swiss-Prot/TrEMBL) for protein sequence searches, FASTA retrieval, functional annotations (GO terms, domains), and cross-database ID mapping. Use when looking up a protein entry, fetching a protein FASTA sequence, or mapping accessions between databases over raw HTTP/REST; for EXPERIMENTAL 3D structures prefer alterlab-pdb, for AI-PREDICTED 3D structures prefer alterlab-alphafold-db, for protein-protein interaction networks prefer alterlab-string-db, and for Python workflows spanning many databases prefer bioservices instead. Part of the AlterLab Academic Skills suite.

Access the ZINC database of 230M+ commercially available (purchasable) compounds, searching by ZINC ID or SMILES, running similarity searches, and downloading 3D-ready structures. Use when assembling a compound library for virtual screening, finding purchasable analogs, or obtaining docking-ready 3D structures for drug discovery. Part of the AlterLab Academic Skills suite.

Access USPTO APIs for patent and trademark searches, examination history (PEDS), assignments, citations, office actions, and trademark status (TSDR). Use when searching patents or trademarks, conducting prior art searches, retrieving patent examination or assignment records, or doing intellectual property (IP) analysis. Part of the AlterLab Academic Skills suite.

Run Open Notebook, a self-hosted open-source alternative to Google NotebookLM with a full REST API, for AI-powered research and document analysis. Use when organizing research materials into notebooks, ingesting diverse content sources (PDFs, videos, audio, web pages, Office documents), generating AI-powered notes and summaries, creating multi-speaker podcasts from research, chatting with documents using context-aware AI, searching across materials with full-text and vector search, or running custom content transformations. Supports 18+ AI providers including OpenAI, Anthropic, Google, Ollama, LM Studio, Groq, and Mistral with complete data privacy through self-hosting. For a one-shot file-to-Markdown conversion (no notebook, chat, or search), use alterlab-markitdown instead. Part of the AlterLab Academic Skills suite.

Explore a single PDF in depth — parse it once, then answer questions across its sections, figures, tables, and appendices — comparing methods across sections, extracting every instance of a pattern within the document, and reading values off its charts and tables. Use when interrogating one paper or report end-to-end, pulling every occurrence of something inside a document, or reading data from a figure/table in a PDF, serving the literature-review and paper-review pipeline. To build a comparison table across MANY papers prefer alterlab-pdf-extract; to simply convert a PDF to Markdown prefer alterlab-markitdown; for reference/citation management prefer alterlab-pyzotero. Part of the AlterLab Academic Skills suite.